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Kokkoris V, Banchini C, Paré L, Abdellatif L, Séguin S, Hubbard K, Findlay W, Dalpé Y, Dettman J, Corradi N, Stefani F. Rhizophagus irregularis, the model fungus in arbuscular mycorrhiza research, forms dimorphic spores. New Phytol 2024; 242:1771-1784. [PMID: 37434339 DOI: 10.1111/nph.19121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/10/2023] [Indexed: 07/13/2023]
Abstract
Rhizophagus irregularis is the model species for arbuscular mycorrhizal fungi (AMF) research and the most widely propagated species for commercial plant biostimulants. Using asymbiotic and symbiotic cultivation systems initiated from single spores, advanced microscopy, Sanger sequencing of the glomalin gene, and PacBio sequencing of the partial 45S rRNA gene, we show that four strains of R. irregularis produce spores of two distinct morphotypes, one corresponding to the morphotype described in the R. irregularis protologue and the other having the phenotype of R. fasciculatus. The two spore morphs are easily distinguished by spore colour, thickness of the subtending hypha, thickness of the second wall layer, lamination of the innermost layer, and the dextrinoid reaction of the two outer spore wall layers to Melzer's reagent. The glomalin gene of the two spore morphs is identical and that of the PacBio sequences of the partial SSU-ITS-LSU region (2780 bp) obtained from single spores of the R. cf fasciculatus morphotype has a median pairwise similarity of 99.8% (SD = 0.005%) to the rDNA ribotypes of R. irregularis DAOM 197198. Based on these results, we conclude that the model AMF species R. irregularis is dimorphic, which has caused taxonomic confusion in culture collections and possibly in AMF research.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Claudia Banchini
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Louis Paré
- Université Laval, Centre d'Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Lobna Abdellatif
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Keith Hubbard
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Wendy Findlay
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
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Bromfield ESP, Cloutier S. Bradyrhizobium ontarionense sp. nov., a novel bacterial symbiont isolated from Aeschynomene indica (Indian jointvetch), harbours photosynthesis, nitrogen fixation and nitrous oxide (N 2O) reductase genes. Antonie Van Leeuwenhoek 2024; 117:69. [PMID: 38647727 PMCID: PMC11035471 DOI: 10.1007/s10482-024-01940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 04/25/2024]
Abstract
A novel bacterial symbiont, strain A19T, was previously isolated from a root-nodule of Aeschynomene indica and assigned to a new lineage in the photosynthetic clade of the genus Bradyrhizobium. Here data are presented for the detailed genomic and taxonomic analyses of novel strain A19T. Emphasis is placed on the analysis of genes of practical or ecological significance (photosynthesis, nitrous oxide reductase and nitrogen fixation genes). Phylogenomic analysis of whole genome sequences as well as 50 single-copy core gene sequences placed A19T in a highly supported lineage distinct from described Bradyrhizobium species with B. oligotrophicum as the closest relative. The digital DNA-DNA hybridization and average nucleotide identity values for A19T in pair-wise comparisons with close relatives were far lower than the respective threshold values of 70% and ~ 96% for definition of species boundaries. The complete genome of A19T consists of a single 8.44 Mbp chromosome and contains a photosynthesis gene cluster, nitrogen-fixation genes and genes encoding a complete denitrifying enzyme system including nitrous oxide reductase implicated in the reduction of N2O, a potent greenhouse gas, to inert dinitrogen. Nodulation and type III secretion system genes, needed for nodulation by most rhizobia, were not detected. Data for multiple phenotypic tests complemented the sequence-based analyses. Strain A19T elicits nitrogen-fixing nodules on stems and roots of A. indica plants but not on soybeans or Macroptilium atropurpureum. Based on the data presented, a new species named Bradyrhizobium ontarionense sp. nov. is proposed with strain A19T (= LMG 32638T = HAMBI 3761T) as the type strain.
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Affiliation(s)
- Eden S P Bromfield
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada.
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada
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3
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Tiwari G, Kaur N, Anderson NP, Tanner KC, Lightle DM, Willette AR, Otani JK, Jorgensen AM, Yoder C, Dorman SJ. Field-evolved pyrethroid resistance in Tychius picirostris (Coleoptera: Curculionidae) populations in Oregon white clover seed crops. J Econ Entomol 2024; 117:609-617. [PMID: 38284646 DOI: 10.1093/jee/toae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The clover seed weevil, Tychius picirostris Fabricius, a serious pest of white clover, Trifolium repens L., grown for seed in western Oregon, causing feeding damage to flowers and developing seeds. Since 2017, white clover seed producers have anecdotally reported T. picirostris control failures using foliar pyrethroid insecticide applications. This mode of action (MoA) is an important chemical control option for T. picirostris management. To evaluate insecticide resistance selection to pyrethroids (bifenthrin) and other MoAs labeled for T. picirostris management (malathion and chlorantraniliprole), adult populations were collected from 8 commercial white clover grown for seed fields in the Willamette Valley, OR, in 2022 and 2023. Among collected Oregon populations, very high resistance ratios (RR50 = 178.00-725.67) were observed to technical grade bifenthrin and low to high resistance ratios (RR50 = 7.80-32.80) to malathion in surface contact assays compared to a susceptible Canadian field population. Moreover, >2.73 times the labeled rate of formulated product containing bifenthrin as the sole MoA was required to kill >50% of T. picirostris in topical assays. Synergistic assays with a mixed-function oxidase inhibitor, an esterase inhibitor, and a glutathione-S-transferase inhibitor revealed phase I and II detoxification enzymes are present in Oregon T. picirostris populations and confer metabolic resistance to bifenthrin. This is the first report of T. picirostris insecticide resistance selection to pyrethroid and organophosphate insecticides. Results will inform continued monitoring and insecticide resistance management strategies to slow the evolution of T. picirostris insecticide resistance selection in Oregon's white clover seed production.
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Affiliation(s)
- Grace Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Navneet Kaur
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Nicole P Anderson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - K Christy Tanner
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Danielle M Lightle
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Alison R Willette
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Jennifer K Otani
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB T0H 0C0, Canada
| | - Amanda M Jorgensen
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB T0H 0C0, Canada
| | - Calvin Yoder
- SARDA Ag Research, Peace Region Forage Seed Association, Falher, AB T0H 1M0, Canada
| | - Seth J Dorman
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
- USDA-ARS, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, USA
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Singleton K, van Herk WG, Pickett C, Blake AJ, Asad S, Furtado K, Saguez J, Gries G. Spectral sensitivity of click beetles (Coleoptera: Elateridae) and their responses to light stimuli in laboratory and field experiments. Environ Entomol 2024; 53:199-212. [PMID: 38284422 DOI: 10.1093/ee/nvad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/12/2023] [Accepted: 02/05/2024] [Indexed: 01/30/2024]
Abstract
With increasingly fewer insecticides registered to control the larvae of pest click beetles (Coleoptera: Elateridae), integrative beetle management, including pheromone- and light-based trapping of adult beetles, must be explored as an alternative strategy. Here, we analyzed the spectral sensitivity and color preference of 9 elaterids across 6 genera in electrophysiological recordings and in behavioral bioassays. In electroretinogram recordings (ERGs), dark-adapted beetles were exposed to narrow wavebands of light in 10-nm increments from 330 to 650 nm. All beetles proved most sensitive to green (515-538 nm) and ultraviolet (UV) light (~360 nm). In 4-choice bioassay arenas with 3 light emitting diodes (LEDs; green [525 nm], blue [470 nm], red [655 nm]) and a dark control as test stimuli, beetles discriminated between test stimuli, being preferentially attracted to green and blue LEDs. In field experiments, Vernon pitfall traps fitted with a green, blue or white LED captured significantly more male and female Agriotes lineatus and A. obscurus than dark control traps. When traps were baited with green or blue LEDs at light intensities that differed by 10-fold, the traps baited with higher light intensity lures captured numerically more beetles but trap catch data in accordance with light intensity did not differ statistically. Light-based trapping may be a viable tool for monitoring elaterid species known not to have pheromones.
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Affiliation(s)
- Kendal Singleton
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A0, Canada
| | - Willem G van Herk
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A0, Canada
| | - Calla Pickett
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Adam James Blake
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Syed Asad
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Kathleen Furtado
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Julien Saguez
- Centre de recherche sur les grains, Saint-Mathieu-de-Beloeil, QC J3G 0E2, Canada
| | - Gerhard Gries
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Pahari S, Vaid N, Soolanayakanahally R, Kagale S, Pasha A, Esteban E, Provart N, Stobbs JA, Vu M, Meira D, Karunakaran C, Boda P, Prasannakumar MK, Nagaraja A, Jain AK. Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense). Plant J 2024. [PMID: 38576267 DOI: 10.1111/tpj.16749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.
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Affiliation(s)
- Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Miranda Vu
- Canadian Light Source Inc, Saskatoon, Saskatchewan, Canada
| | - Debora Meira
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, United States
| | | | - Praveen Boda
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | | | - Alur Nagaraja
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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Peirson M, Ibrahim A, Ovinge LP, Hoover SE, Guarna MM, Melathopoulos A, Pernal SF. The effects of protein supplementation, fumagillin treatment, and colony management on the productivity and long-term survival of honey bee (Apis mellifera) colonies. PLoS One 2024; 19:e0288953. [PMID: 38489327 PMCID: PMC10942092 DOI: 10.1371/journal.pone.0288953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 11/24/2023] [Indexed: 03/17/2024] Open
Abstract
In this study, we intensively measured the longitudinal productivity and survival of 362 commercially managed honey bee colonies in Canada, over a two-year period. A full factorial experimental design was used, whereby two treatments were repeated across apiaries situated in three distinct geographic regions: Northern Alberta, Southern Alberta and Prince Edward Island, each having unique bee management strategies. In the protein supplemented treatment, colonies were continuously provided a commercial protein supplement containing 25% w/w pollen, in addition to any feed normally provided by beekeepers in that region. In the fumagillin treatment, colonies were treated with the label dose of Fumagilin-B® each year during the fall. Neither treatment provided consistent benefits across all sites and dates. Fumagillin was associated with a large increase in honey production only at the Northern Alberta site, while protein supplementation produced an early season increase in brood production only at the Southern Alberta site. The protein supplement provided no long-lasting benefit at any site and was also associated with an increased risk of death and decreased colony size later in the study. Differences in colony survival and productivity among regions, and among colonies within beekeeping operations, were far larger than the effects of either treatment, suggesting that returns from extra feed supplements and fumagillin were highly contextually dependent. We conclude that use of fumagillin is safe and sometimes beneficial, but that beekeepers should only consider excess protein supplementation when natural forage is limiting.
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Affiliation(s)
- Michael Peirson
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Abdullah Ibrahim
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Lynae P. Ovinge
- Alberta Agriculture and Forestry, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Shelley E. Hoover
- Alberta Agriculture and Forestry, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - M. Marta Guarna
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Andony Melathopoulos
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stephen F. Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
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Wang M, Bissonnette N, Laterrière M, Dudemaine PL, Gagné D, Roy JP, Sirard MA, Ibeagha-Awemu EM. DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits. BMC Biol 2024; 22:65. [PMID: 38486242 PMCID: PMC10941392 DOI: 10.1186/s12915-024-01843-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND DNA methylation has been documented to play vital roles in diseases and biological processes. In bovine, little is known about the regulatory roles of DNA methylation alterations on production and health traits, including mastitis. RESULTS Here, we employed whole-genome DNA methylation sequencing to profile the DNA methylation patterns of milk somatic cells from sixteen cows with naturally occurring Staphylococcus aureus (S. aureus) subclinical mastitis and ten healthy control cows. We observed abundant DNA methylation alterations, including 3,356,456 differentially methylated cytosines and 153,783 differential methylation haplotype blocks (dMHBs). The DNA methylation in regulatory regions, including promoters, first exons and first introns, showed global significant negative correlations with gene expression status. We identified 6435 dMHBs located in the regulatory regions of differentially expressed genes and significantly correlated with their corresponding genes, revealing their potential effects on transcriptional activities. Genes harboring DNA methylation alterations were significantly enriched in multiple immune- and disease-related pathways, suggesting the involvement of DNA methylation in regulating host responses to S. aureus subclinical mastitis. In addition, we found nine discriminant signatures (differentiates cows with S. aureus subclinical mastitis from healthy cows) representing the majority of the DNA methylation variations related to S. aureus subclinical mastitis. Validation of seven dMHBs in 200 cows indicated significant associations with mammary gland health (SCC and SCS) and milk production performance (milk yield). CONCLUSIONS In conclusion, our findings revealed abundant DNA methylation alterations in milk somatic cells that may be involved in regulating mammary gland defense against S. aureus infection. Particularly noteworthy is the identification of seven dMHBs showing significant associations with mammary gland health, underscoring their potential as promising epigenetic biomarkers. Overall, our findings on DNA methylation alterations offer novel insights into the regulatory mechanisms of bovine subclinical mastitis, providing further avenues for the development of effective control measures.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Université de Montréal, St-Hyacinthe, QC, Canada
| | | | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
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Wang M, Yang N, Laterrière M, Gagné D, Omonijo F, Ibeagha-Awemu EM. Multi-omics integration identifies regulatory factors underlying bovine subclinical mastitis. J Anim Sci Biotechnol 2024; 15:46. [PMID: 38481273 PMCID: PMC10938844 DOI: 10.1186/s40104-024-00996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/14/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry. Multi-omics approaches enable the comprehensive investigation of the complex interactions between multiple layers of information to provide a more holistic view of disease pathogenesis. Therefore, this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data (mRNA and lncRNA), small RNA sequencing data (miRNA) and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes. RESULTS Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis, provided further insights into subclinical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis. The abundant genomic and epigenomic signatures with significant alterations related to subclinical mastitis were observed, including 30,846, 2552, 1276 and 57 differential methylation haplotype blocks (dMHBs), differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs), respectively. Next, 5 factors presenting the principal variation of differential multi-omics signatures were identified. The important roles of Factor 1 (DEG, DEM and DEL) and Factor 2 (dMHB and DEM), in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed. Each of the omics within Factors 1 and 2 explained about 20% of the source of variation in subclinical mastitis. Also, networks of important functional gene sets with the involvement of multi-omics signatures were demonstrated, which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis. Furthermore, multi-omics integration enabled the association of the epigenomic regulatory factors (dMHBs, DELs and DEMs) of altered genes in important pathways, such as 'Staphylococcus aureus infection pathway' and 'natural killer cell mediated cytotoxicity pathway', etc., which provides further insights into mastitis regulatory mechanisms. Moreover, few multi-omics signatures (14 dMHBs, 25 DEGs, 18 DELs and 5 DEMs) were identified as candidate discriminant signatures with capacity of distinguishing subclinical mastitis cows from healthy cows. CONCLUSION The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis, which may ultimately lead to the development of more effective mastitis control and management strategies.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Université Laval, Quebec City, QC, Canada
| | - Naisu Yang
- Department of Animal Science, Université Laval, Quebec City, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Faith Omonijo
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.
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O'Hara E, Zaheer R, Andrés-Lasheras S, McAllister TA, Gruninger RJ. Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction. FEMS Microbiol Ecol 2024; 100:fiae002. [PMID: 38373802 PMCID: PMC10960635 DOI: 10.1093/femsec/fiae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024] Open
Abstract
Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.
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Affiliation(s)
- Eóin O'Hara
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Sara Andrés-Lasheras
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
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Gonçalves Vero J, Devillers N, Bridi AM, Moak KAT, Aboagye G, Agostinis Ferreira G, Genova JL, Conte S, Faucitano L. Correction: Gonçalves Vero et al. Transport of Pigs of Two Market Weights at Two Space Allowances: Effects on Behaviour, Blood Parameters, and Meat Quality under Summer and Winter Conditions. Animals 2023, 13, 2767. Animals (Basel) 2024; 14:810. [PMID: 38473204 DOI: 10.3390/ani14050810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
In the original publication [...].
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Affiliation(s)
- Jessica Gonçalves Vero
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
- Departamento de Zootecnia, Universidade Estadual de Londrina, Londrina 86051-990, Brazil
| | - Nicolas Devillers
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Ana Maria Bridi
- Departamento de Zootecnia, Universidade Estadual de Londrina, Londrina 86051-990, Brazil
| | - Kyle A T Moak
- Department of Animal Science, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Gizella Aboagye
- European Food Safety Authority (EFSA), Via Carlo Magno 1A, 43126 Parma, Italy
| | | | - Jansller Luiz Genova
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Sabine Conte
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Luigi Faucitano
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
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11
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Sheikh AA, Schneiderman D, Sykes EME, Kumar A, Chen W, Lapen DR, Khan IUH. Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species. Lett Appl Microbiol 2024; 77:ovae027. [PMID: 38460955 DOI: 10.1093/lambio/ovae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.
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Affiliation(s)
- Alexander A Sheikh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
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12
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Hu H, Zhang Y, Yu F. A CRISPR/Cas9-based vector system enables the fast breeding of selection-marker-free canola with Rcr1-rendered clubroot resistance. J Exp Bot 2024; 75:1347-1363. [PMID: 37991105 PMCID: PMC10901203 DOI: 10.1093/jxb/erad471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Breeding for disease resistance in major crops is of crucial importance for global food security and sustainability. However, common biotechnologies such as traditional transgenesis or genome editing do not provide an ideal solution, whereas transgenic crops free of selection markers such as cisgenic/intragenic crops might be suitable. In this study, after cloning and functional verification of the Rcr1 gene for resistance to clubroot (Plasmodiophora brassicae), we confirmed that the genes Rcr1, Rcr2, Rcr4, and CRa from Brassica rapa crops and the resistance gene from B. napus oilseed rape cv. 'Mendel' on chromosome A03 were identical in their coding regions. We also determined that Rcr1 has a wide distribution in Brassica breeding materials and renders potent resistance against multiple representative clubroot strains in Canada. We then modified a CRISPR/Cas9-based cisgenic vector system and found that it enabled the fast breeding of selection-marker-free transgenic crops with add-on traits, with selection-marker-free canola (B. napus) germplasms with Rcr1-rendered stable resistance to clubroot disease being successfully developed within 2 years. In the B. napus background, the intragenic vector system was able to remove unwanted residue sequences from the final product with high editing efficiency, and off-target mutations were not detected. Our study demonstrates the potential of applying this breeding strategy to other crops that can be transformed by Agrobacterium. Following the streamlined working procedure, intragenic germplasms can be developed within two generations, which could significantly reduce the breeding time and labor compared to traditional introgression whilst still achieving comparable or even better breeding results.
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Affiliation(s)
- Hao Hu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yan Zhang
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
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13
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Witte T, Hicks C, Hermans A, Shields S, Overy DP. Debunking the Myth of Fusarium poae T-2/HT-2 Toxin Production. J Agric Food Chem 2024; 72:3949-3957. [PMID: 38375818 PMCID: PMC10905990 DOI: 10.1021/acs.jafc.3c08437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/21/2024]
Abstract
Fusarium poae is commonly detected in field surveys of Fusarium head blight (FHB) of cereal crops and can produce a range of trichothecene mycotoxins. Although experimentally validated reports of F. poae strains producing T-2/HT-2 trichothecenes are rare, F. poae is frequently generalized in the literature as a producer of T-2/HT-2 toxins due to a single study from 2004 in which T-2/HT-2 toxins were detected at low levels from six out of forty-nine F. poae strains examined. To validate/substantiate the observations reported from the 2004 study, the producing strains were acquired and phylogenetically confirmed to be correctly assigned as F. poae; however, no evidence of T-2/HT-2 toxin production was observed from axenic cultures. Moreover, no evidence for a TRI16 ortholog, encoding a key acyltransferase shown to be necessary for T-2 toxin production in other Fusarium species, was observed in any of the de novo assembled genomes of the F. poae strains. Our findings corroborate multiple field-based and in vitro studies on FHB-associated Fusarium populations which also do not support the production of T-2/HT-2 toxins with F. poae and therefore conclude that F. poae should not be generalized as a T-2/HT-2 toxin producing species of Fusarium.
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Affiliation(s)
- Thomas
E. Witte
- Agriculture
and Agri-Food Canada, Ottawa Research and
Development Centre, Ottawa, Ontario K1A 0C6, Canada
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Carmen Hicks
- Agriculture
and Agri-Food Canada, Ottawa Research and
Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Anne Hermans
- Agriculture
and Agri-Food Canada, Ottawa Research and
Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Sam Shields
- Agriculture
and Agri-Food Canada, Ottawa Research and
Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - David P. Overy
- Agriculture
and Agri-Food Canada, Ottawa Research and
Development Centre, Ottawa, Ontario K1A 0C6, Canada
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14
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Almashhadany DA, Hassan AA, Rashid RF, Abdulmawjood A, Khan IUH. Assessment and Assay Comparison for Detection of Antimicrobial Residues in Freshwater Aquaculture Fish in Erbil Governorate, Iraq. Antibiotics (Basel) 2024; 13:225. [PMID: 38534660 DOI: 10.3390/antibiotics13030225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The excessive and uncontrolled application of antibiotics in the fish farming industry, coupled with a lack of health monitoring and medication practices, is a driving force behind the escalating development of antimicrobial resistance. The present study assessed and compared qualitative field diffusion (QFD) and disk diffusion (DD) assays for the detection of antimicrobial residues (ARs) in diverse freshwater aquaculture fish. A total of 380 freshwater aquaculture fish (160 fresh and 180 frozen) samples were systematically collected between January and June 2021 from various retail stores located in Erbil Governorate, Iraq. Based on QFDA results, overall, ARs were detected (52; 15.3%) at a relatively lower frequency with comparatively higher frequency (21; 31.1%) in fresh than (31; 17.2%) frozen fish samples. On the other hand, DDA also revealed a comparable (45; 13.2%) prevalence rate of ARs. However, a low detection was observed more in fresh (17; 10.6%) than frozen (28; 15.6%) fish samples. Moreover, no statistically significant disparity (χ2 = 0.069; p = 0.79) between two assays and types of fish was recorded. In conclusion, the results of the present study showed that detecting a considerable frequency of ARs in these fish samples raises concerns about potential threats to public health. This underscores the necessity for understanding antibiotic application in aquaculture and its potential connection to antibiotic resistance in bacterial pathogens. Such comprehension is pivotal for formulating and implementing effective control and farm management strategies to address this pressing issue.
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Affiliation(s)
- Dhary Alewy Almashhadany
- Department of Medical Laboratory Science, College of Science, Knowledge University, Erbil 44001, Iraq
| | - Abdulwahed Ahmed Hassan
- Metedi Medical Technology Distributions, Rathenaustraße 2, 35394 Giessen, Germany
- Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, University of Mosul, Mosul 41002, Iraq
| | - Rzgar Farooq Rashid
- Department of Medical Laboratory Science, College of Science, Knowledge University, Erbil 44001, Iraq
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
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15
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Babarinde S, Burlakoti RR, Peters RD, Al-Mughrabi K, Novinscak A, Sapkota S, Prithiviraj B. Genetic structure and population diversity of Phytophthora infestans strains in Pacific western Canada. Appl Microbiol Biotechnol 2024; 108:237. [PMID: 38407622 PMCID: PMC10896882 DOI: 10.1007/s00253-024-13040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/07/2024] [Accepted: 01/28/2024] [Indexed: 02/27/2024]
Abstract
Late blight caused by Phytophthora infestans is an economically important disease of potato and tomato worldwide. In Canada, an increase in late blight incidence and severity coincided with changes in genetic composition of P. infestans. We monitored late blight incidence on tomato and potato in Pacific western and eastern Canada between 2019 and 2022, identified genotypes of P. infestans, and examined their population genetic diversity. We identified four major existing genotypes US11, US17, US8, and US23 as well as 25 new genotypes. The US11 genotype was dominant in Pacific western Canada, accounting for 59% of the total population. We discovered the US17 genotype for the first time in Canada. We revealed a higher incidence of late blight and quite diverse genotypes of P. infestans in Pacific western Canada than in eastern Canada. We found high genetic diversity of P. infestans population from Pacific western Canada, as evidenced by the high number of multilocus genotypes, high values of genetic diversity indices, and emergence of 25 new genotypes. Considering the number of disease incidence, the detection of diverse known genotypes, the emergence of novel genotypes, and the high number of isolates resistant to metalaxyl-m (95%) from Pacific western Canada, the region could play a role in establishing sexual recombination and diverse populations, which could ultimately pose challenges for late blight management. Therefore, continuous monitoring of P. infestans populations in Pacific western region and across Canada is warranted. KEY POINTS: • Genotypes of P. infestans in Pacific western were quite diverse than in eastern Canada. • We discovered US17 genotype for the first time in Canada and identified 26 novel genotypes. • Approximately 95% of P. infestans isolates were resistant to metalaxyl-m.
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Affiliation(s)
- Segun Babarinde
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, 6947 Hwy 7, Agassiz, BC, V0M 1A0, Canada
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Rishi R Burlakoti
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, 6947 Hwy 7, Agassiz, BC, V0M 1A0, Canada.
| | - Rick D Peters
- Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE, C1A 4N6, Canada
| | - Khalil Al-Mughrabi
- New Brunswick Department of Agriculture, Aquaculture and Fisheries, 39 Barker Lane, Wicklow, NB, E7L 3S4, Canada
| | - Amy Novinscak
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, 6947 Hwy 7, Agassiz, BC, V0M 1A0, Canada
| | - Sanjib Sapkota
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, 6947 Hwy 7, Agassiz, BC, V0M 1A0, Canada
| | - Balakrishnan Prithiviraj
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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16
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Aiyer HS, McKenzie-Gopsill A, Mills A, Foster AJ. Select Cover Crop Residue and Soil Microbiomes Contribute to Suppression of Fusarium Root and Crown Rot in Barley and Soybean. Microorganisms 2024; 12:404. [PMID: 38399808 PMCID: PMC10891762 DOI: 10.3390/microorganisms12020404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Fusarium root and crown rot (FRCR) negatively impact several economically important plant species. Cover crops host different soil and residue microbiomes, thereby potentially influencing pathogen load and disease severity. The carryover effect of cover crops on FRCR in barley and soybean was investigated. Field trials were conducted in Prince Edward Island, Canada. Two cover crops from each plant group, including forbs, brassicas, legumes, and grasses, were grown in a randomized complete block design with barley and soybean planted in split plots the following year. Barley and soybean roots were assessed for FRCR through visual disease rating and Fusarium spp. were isolated from diseased tissue. Fungal and bacterial communities in cover crop residues were quantified using amplicon sequencing. The disease-suppressive effects of soil were tested in greenhouse studies. The results indicated that sorghum-sudangrass-associated microbiomes suppress Fusarium spp., leading to reduced FRCR in both barley and soybean. The oilseed radish microbiome had the opposite effect, consequently increasing FRCR incidence in barley and soybean. The results from this study indicate that cover crop residue and the associated soil microbiome influence the incidence and severity of FRCR in subsequent crops. This information can be used to determine cover cropping strategies in barley and soybean production systems.
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Affiliation(s)
- Harini S. Aiyer
- Agassiz Research and Development Center, Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A2, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew McKenzie-Gopsill
- Charlottetown Research and Development Center, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
| | - Aaron Mills
- Charlottetown Research and Development Center, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
| | - Adam John Foster
- Charlottetown Research and Development Center, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
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17
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Lau CHF, Capitani S, Tien YC, Verellen LA, Kithama M, Kang H, Kiarie EG, Topp E, Diarra MS, Fruci M. Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens. Anim Microbiome 2024; 6:6. [PMID: 38360706 PMCID: PMC10868003 DOI: 10.1186/s42523-024-00293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds. RESULTS Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet. CONCLUSIONS Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.
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Affiliation(s)
- Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
| | - Sabrina Capitani
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Yuan-Ching Tien
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Munene Kithama
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Hellen Kang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Agroécologie research unit, INRAE, Université de Bourgogne, Dijon, France
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada.
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18
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Colwell MJ, Pernal SF, Currie RW. Treatment of waxborne honey bee (Hymenoptera: Apidae) viruses using time, temperature, and electron-beam irradiation. J Econ Entomol 2024; 117:34-42. [PMID: 38206826 PMCID: PMC10860154 DOI: 10.1093/jee/toad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 01/13/2024]
Abstract
Viruses are one of many serious threats to honey bee (Apis mellifera L.) health. There are many transmission routes for honey bee viruses, and there is potential for wax comb to act as a reservoir for transmission of viruses. Some work has been done on treating viruses on wax, focusing on irradiation as a potential treatment. However, irradiation is not universally available or economically viable for beekeepers in many regions. With increased colony deaths over winter beekeepers potentially risk further loss from reusing contaminated equipment from dead colonies. Here we explored the use of storage time and temperature on the reduction of waxborne virus levels from winter loss colony wax over 30 days and at -20, 5, and 20 °C. Furthermore, because irradiation has previously worked against waxborne viruses, we performed a dosage experiment with electron-beam irradiation. Winter loss wax was again used, and exposed to 10, 25, 35, and 45 kGy irradiation, including a nonirradiated transport control. Storage time decreased abundance of black queen cell virus and deformed wing virus at times equal or greater than 30 days but temperatures had no significant effect on virus levels. All irradiation doses decreased virus abundance and prevalence, yet only 35 and 45 kGy did so at a greater rate than the effect of transport alone.
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Affiliation(s)
- Megan J Colwell
- Department of Entomology, Faculty of Agriculture and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Stephen F Pernal
- Department of Entomology, Faculty of Agriculture and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB, Canada
| | - Robert W Currie
- Department of Entomology, Faculty of Agriculture and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
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19
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Nguyen HDT, Ponomareva E, Dadej K, Smith D, Antoun M, van der Lee TAJ, van de Vossenberg BTLH. A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences. PLoS One 2024; 19:e0296842. [PMID: 38346034 PMCID: PMC10861067 DOI: 10.1371/journal.pone.0296842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/19/2023] [Indexed: 02/15/2024] Open
Abstract
Potato wart disease is caused by the obligate fungal pathogen Synchytrium endobioticum. DNA extraction from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes often results in low S. endobioticum DNA concentration or highly contaminated with DNA coming from other microorganisms and the potato host. Therefore, Illumina sequencing of these samples generally results in suboptimal recovery of the nuclear genome sequences of S. endobioticum. A hybridization-based target enrichment protocol was developed to strongly enhance the recovery of S. endobioticum DNA while off-target organisms DNA remains uncaptured. The design strategy involved creating a set of 180,000 molecular baits targeting both gene and non-gene regions of S. endobioticum. The baits were applied to whole genome amplified DNA samples of various S. endobioticum pathotypes (races) in compost, from purified spores and crude wart tissue samples. This was followed by Illumina sequencing and bioinformatic analyses. Compared to non-enriched samples, target enriched samples: 1) showed a significant increase in the proportion of sequenced bases mapped to the S. endobioticum nuclear genome, especially for crude wart tissue samples; 2) yielded sequencing data with higher and better nuclear genome coverage; 3) biased genome assembly towards S. endobioticum sequences, yielding smaller assembly sizes but higher representation of putative S. endobioticum contigs; 4) showed an increase in the number of S. endobioticum genes detected in the genome assemblies. Our hybridization-based target enrichment protocol offers a valuable tool for enhancing genome sequencing and NGS-based molecular detection of S. endobioticum, especially in difficult samples.
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Affiliation(s)
- Hai D. T. Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ekaterina Ponomareva
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kasia Dadej
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Donna Smith
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Prince Edward Island, Canada
| | - Melissa Antoun
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Prince Edward Island, Canada
| | - Theo A. J. van der Lee
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Bart T. L. H. van de Vossenberg
- Netherlands Institute for Vectors, Invasive Plants and Plant Health, Dutch National Plant Protection Organization, Wageningen, the Netherlands
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Mousavi SE, Goyette B, Zhao X, Couture C, Talbot G, Rajagopal R. Struvite-Driven Integration for Enhanced Nutrient Recovery from Chicken Manure Digestate. Bioengineering (Basel) 2024; 11:145. [PMID: 38391631 PMCID: PMC10886100 DOI: 10.3390/bioengineering11020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
This study investigated the synergistic integration of clean technologies, specifically anaerobic digestion (AD) and struvite precipitation, to enhance nutrient recovery from chicken manure (CM). The batch experiments were conducted using (i) anaerobically digested CM digestate, referred to as raw sample (RS), (ii) filtered digestate sample (FS), and (iii) a synthetically prepared control sample (CS). The research findings demonstrated that the initial ammonia concentration variations did not significantly impact the struvite precipitation yield in the RS and FS, showcasing the materials inertness process's robustness to changing ammonia concentrations. Notably, the study revealed that the highest nitrogen (N) recovery, associated with 86% and 88% ammonia removal in the CS and FS, was achieved at pH 11, underscoring the efficiency of nutrient recovery. The RS achieved the highest nitrogen recovery efficiency at pH 10, at 86.3%. In addition, the research highlighted the positive impact of reducing heavy metal levels (Zn, Cu, Pb, Ni, Cd, Cr and Fe) and improving the composition of the microbial community in the digestate. These findings offer valuable insights into sustainable manure and nutrient management practices, emphasizing the potential benefits for the agricultural sector and the broader circular economy. Future research directions include economic viability assessments, regulatory compliance evaluations, and knowledge dissemination to promote the widespread adoption of these clean technologies on a larger scale. The study marks a significant step toward addressing the environmental concerns associated with poultry farming and underscores the potential of integrating clean technologies for a more sustainable agricultural future.
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Affiliation(s)
- Seyyed Ebrahim Mousavi
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
- Department of Animal Science, McGill University, 21111 Lakeshore Road, Saint Anne De Bellevue, QC H9X 3V9, Canada
| | - Bernard Goyette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, 21111 Lakeshore Road, Saint Anne De Bellevue, QC H9X 3V9, Canada
| | - Cassandra Couture
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
- Department of Biology, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Guylaine Talbot
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
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Avramov M, Gallo V, Gross A, Lapen DR, Ludwig A, Cullingham CI. A cost-effective RNA extraction and RT-qPCR approach to detect California serogroup viruses from pooled mosquito samples. Sci Rep 2024; 14:2339. [PMID: 38281985 PMCID: PMC10822844 DOI: 10.1038/s41598-024-52534-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/19/2024] [Indexed: 01/30/2024] Open
Abstract
Mosquito-borne diseases pose ongoing global health concerns, demanding more cost-efficient methods to detect pathogens to support enhanced surveillance efforts. This study introduces an adapted TRIzol-based high-throughput RNA extraction protocol, tailored for the detection of California serogroup viruses in pooled mosquito samples in a rapid and cost-effective manner. This approach provided consistent RNA yields and sensitive viral detection relative to two commercial extraction kits (QIAGEN RNeasy Mini Kit and MACHEREY-NAGEL NucleoSpin RNA Plus Kit). The incorporation of a user-friendly and non-spiking-based RT-qPCR internal control designed for the 18S rRNA gene in mosquitoes minimizes potential false positives/negatives, improving the fidelity of viral detection outcomes. Effective RNA yields, purity, and successful target amplification across 25 mosquito species and varied pool sizes (1-50 mosquitoes per tube) affirm the reliability of our approach. The extraction method is cost-effective, with an incurred cost of $0.58 CAD per sample, in contrast to the $5.25 CAD cost per sample of the two kits, rendering it promising for mosquito-borne disease surveillance initiatives.
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Affiliation(s)
- Marc Avramov
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
- National Microbiology Laboratory Branch, Public Health Agency of Canada, 3200 Rue Sicotte, C.P. 5000, St. Hyacinthe, QC, J2S 2M2, Canada.
| | - Vanessa Gallo
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Antonia Gross
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Antoinette Ludwig
- National Microbiology Laboratory Branch, Public Health Agency of Canada, 3200 Rue Sicotte, C.P. 5000, St. Hyacinthe, QC, J2S 2M2, Canada
| | - Catherine I Cullingham
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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22
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Sharma JS, Che M, Fetch T, McCallum BD, Xu SS, Hiebert CW. Identification of Sr67, a new gene for stem rust resistance in KU168-2 located close to the Sr13 locus in wheat. Theor Appl Genet 2024; 137:30. [PMID: 38265482 PMCID: PMC10808535 DOI: 10.1007/s00122-023-04530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
KEY MESSAGE Sr67 is a new stem rust resistance gene that represents a new resource for breeding stem rust resistant wheat cultivars Re-appearance of stem rust disease, caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), in different parts of Europe emphasized the need to develop wheat varieties with effective resistance to local Pgt populations and exotic threats. A Kyoto University wheat (Triticum aestivum L.) accession KU168-2 was reported to carry good resistance to leaf and stem rust. To identify the genomic region associated with the KU168-2 stem rust resistance, a genetic study was conducted using a doubled haploid (DH) population from the cross RL6071 × KU168-2. The DH population was phenotyped with three Pgt races (TTKSK, TPMKC, and QTHSF) and genotyped using the Illumina 90 K wheat SNP array. Linkage mapping showed the resistance to all three Pgt races was conferred by a single stem rust resistance (Sr) gene on chromosome arm 6AL, associated with Sr13. Presently, four Sr13 resistance alleles have been reported. Sr13 allele-specific KASP and STARP markers, and sequencing markers all showed null alleles in KU168-2. KU168-2 showed a unique combination of seedling infection types for five Pgt races (TTKSK, QTHSF, RCRSF, TMRTF, and TPMKC) compared to Sr13 alleles. The phenotypic uniqueness of the stem rust resistance gene in KU168-2 and null alleles for Sr13 allele-specific markers showed the resistance was conferred by a new gene, designated Sr67. Since Sr13 is less effective in hexaploid background, Sr67 will be a good source of stem rust resistance in bread wheat breeding programs.
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Affiliation(s)
- Jyoti Saini Sharma
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Thomas Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Steven S Xu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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23
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Semnani-Azad Z, Wang WZN, Cole DEC, Johnston LW, Wong BYL, Fu L, Retnakaran R, Harris SB, Hanley AJ. Urinary Vitamin D Binding Protein: A Marker of Kidney Tubular Dysfunction in Patients at Risk for Type 2 Diabetes. J Endocr Soc 2024; 8:bvae014. [PMID: 38352963 PMCID: PMC10862653 DOI: 10.1210/jendso/bvae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 02/16/2024] Open
Abstract
Context Recent studies have reported elevated urinary vitamin D binding protein (uVDBP) concentrations in patients with diabetic kidney disease, although the utility of uVDBP to predict deterioration of kidney function over time has not been examined. Objective Our objective was to assess the association of uVDBP with longitudinal changes in kidney function. Methods Adults at-risk for type 2 diabetes from the Prospective Metabolism and Islet Cell Evaluation (PROMISE) study had 3 assessments over 6 years (n = 727). Urinary albumin-to-creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR) were used as measures of kidney function. Measurements of uVDBP were performed with enzyme-linked immunosorbent assay and normalized to urine creatinine (uVDBP:cr). Generalized estimating equations (GEEs) evaluated longitudinal associations of uVDBP and uVDBP:cr with measures of kidney function, adjusting for covariates. Results Renal uVDBP loss increased with ACR severity at baseline. Individuals with normoalbuminuria, microalbuminuria, and macroalbuminuria had median log uVDBP:cr concentrations of 1.62 μg/mmol, 2.63 μg/mmol, and 2.48 μg/mmol, respectively, and ACR positively correlated with uVDBP concentrations (r = 0.37; P < .001). There was no significant association between uVDBP and eGFR at baseline. Adjusted longitudinal GEE models indicated that each SD increase both in baseline and longitudinal uVDBP:cr was significantly associated with higher ACR over 6 years (β = 30.67 and β = 32.91, respectively). Conversely, neither baseline nor longitudinal uVDBP:cr measures showed a significant association with changes in eGFR over time. These results suggest that loss of uVDBP:cr over time may be a useful marker for predicting renal tubular damage in individuals at risk for diabetes.
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Affiliation(s)
- Zhila Semnani-Azad
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Windy Z N Wang
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David E C Cole
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Pediatrics (Genetics), University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Luke W Johnston
- Department of Public Health, Aarhus University, Aarhus 8000, Denmark
| | - Betty Y L Wong
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Lei Fu
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ravi Retnakaran
- Division of Endocrinology and Metabolism, University of Toronto, Toronto, ON M5S 1A8, Canada
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Stewart B Harris
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Anthony J Hanley
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Endocrinology and Metabolism, University of Toronto, Toronto, ON M5S 1A8, Canada
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A8, Canada
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24
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Avramov M, Thaivalappil A, Ludwig A, Miner L, Cullingham CI, Waddell L, Lapen DR. Relationships between water quality and mosquito presence and abundance: a systematic review and meta-analysis. J Med Entomol 2024; 61:1-33. [PMID: 37832159 PMCID: PMC10784781 DOI: 10.1093/jme/tjad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Mosquito-borne diseases (MBDs) are emerging in response to climate and land use changes. As mosquito (Diptera: Culicidae) habitat selection is often contingent on water availability for egg and larval development, studies have recognized water quality also influences larval habitats. However, underlying species-, genera-, and mosquito level preferences for water quality conditions are varied. This systematic review and meta-analysis aimed to identify, characterize, appraise, and synthesize available global data on the relationships between water quality and mosquito presence and abundance (MPA); with the goal to further our understanding of the geographic expansion of MBD risks. A systematic review was conducted to identify studies investigating the relationships between water quality properties and MPA. Where appropriate, random-effects meta-analyses were conducted to provide pooled estimates for the association between the most reported water quality properties and MPA. The most reported water quality parameters were pH (87%), nitrogen concentrations (56%), turbidity (56%), electrical conductivity (54%), dissolved oxygen (43%), phosphorus concentrations (30%), and alkalinity (10%). Overall, pH (P = 0.05), turbidity (P < 0.0001), electrical conductivity (P = 0.005), dissolved oxygen (P < 0.0001), nitrogen (P < 0.0001), and phosphorus (P < 0.0001) showed significantly positive pooled correlations with MPA, while alkalinity showed a nonsignificant null pooled correlation (P = 0.85). We observed high heterogeneity in most meta-analyses, and climate zonation was shown to influence the pooled estimates. Linkages between MPA and water quality properties will enhance our capacity to predict MBD risks under changing environmental and land use changes.
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Affiliation(s)
- Marc Avramov
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
- National Microbiology Laboratory Branch, Public Health Agency of Canada, 3200 rue Sicotte, C.P. 5000, St. Hyacinthe, QC J2S 2M2, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Abhinand Thaivalappil
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Antoinette Ludwig
- National Microbiology Laboratory Branch, Public Health Agency of Canada, 3200 rue Sicotte, C.P. 5000, St. Hyacinthe, QC J2S 2M2, Canada
| | - Lauren Miner
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Catherine I Cullingham
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Lisa Waddell
- National Microbiology Laboratory Branch, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, ON N1H 7M7, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
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25
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Khan IUH, Chen W, Cloutier M, Lapen DR, Craiovan E, Wilkes G. Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water. BMC Microbiol 2024; 24:17. [PMID: 38191309 PMCID: PMC10773081 DOI: 10.1186/s12866-023-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites. RESULTS All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic. CONCLUSIONS The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.
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Affiliation(s)
- Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
| | - Wen Chen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Natural Resources Canada, Ottawa, ON, Canada
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26
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Peirson M, Pernal SF. A Systematic Review of Fumagillin Field Trials for the Treatment of Nosema Disease in Honeybee Colonies. Insects 2024; 15:29. [PMID: 38249035 PMCID: PMC10816105 DOI: 10.3390/insects15010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024]
Abstract
This article systematically reviews controlled field trials of fumagillin dicyclohexylamine in honeybee colonies to determine whether fumagillin effectively controls nosema and whether it is beneficial to colonies. Fifty publications were found that described controlled field trials of fumagillin in honeybee colonies between 1952 and 2023. Fumagillin consistently reduced the prevalence and severity of nosema infections. Doses applied in recent studies were similar to or below those recommended historically. Furthermore, our study showed no negative effects on colony health. Improvements in colony survival, size, and honey production have been demonstrated frequently, though not consistently, in both historic and recent studies. Nevertheless, some practices are not optimal. Treatment decision thresholds based on the number of spores per bee are not well supported by evidence and may be no better than calendar-based prophylactic treatments. In addition, reasonable recommendations to employ quarantine and disinfection procedures together with fumagillin treatment do not appear to have been widely adopted. When used as stand-alone treatments, both the fall- and spring-label doses provide benefits but may be too low and short-term to ensure full control of the disease.
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Affiliation(s)
- Michael Peirson
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - Stephen F. Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
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Li YY, Yaylayan V, Palin MF, Ngapo TM, Cliche S, Sabik H, Gariépy C. Dual effects of dietary carnosine during in vitro digestion of a Western meal model with added ascorbic acid. J Food Sci 2024; 89:710-726. [PMID: 38146794 DOI: 10.1111/1750-3841.16854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 12/27/2023]
Abstract
The beneficial role of carnosine during in vitro digestion of meat was previously demonstrated, and it was hypothesized that such benefits could also be obtained in a meal system. The current study, therefore, assessed carnosine effects on markers of lipid and protein oxidation and of advanced glycation end products (AGEs) during gastric and duodenal in vitro digestion of a burger meal model. The model included intrinsic (low) and enhanced (medium and high) carnosine levels in a mix of pork mince and bread, with or without ascorbic acid (AA) and/or fructose as anti- and prooxidants, respectively. In the presence of either AA or fructose, a carnosine prooxidative potential during digestion was observed at the medium carnosine level depending on markers and digestive phases. However, free carnosine found at the high carnosine level exerted a protective effect reducing the formation of 4-hydroxynonenal in the gastric phase and glyoxal in both the gastric and duodenal phases. Dual effects of carnosine are likely concentration related, whereby at the medium level, free radical production increases through carnosine's ferric-reducing capacity, but there is insufficient quantity to reduce the resulting oxidation, while at the higher carnosine level some decreases in oxidation are observed. In order to obtain carnosine benefits during meal digestion, these findings demonstrate that consideration must be given to the amount and nature of other anti- and prooxidants present and any potential interactions. PRACTICAL APPLICATION: Carnosine, a natural compound in meat, is a multifunctional and beneficial molecule for health. However, both pro- and antioxidative effects of carnosine were observed during digestion of a model burger meal when ascorbic acid was included at a supplemental level. Therefore, to obtain benefits of dietary carnosine during digestion of a meal, consideration needs to be given to the amount and nature of all anti- and prooxidants present and any potential interactions.
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Affiliation(s)
- Yi Yao Li
- Department of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Ste Anne de Bellevue, Québec, Canada
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada
| | - Varoujan Yaylayan
- Department of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Marie-France Palin
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Québec, Canada
| | - Tania M Ngapo
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada
| | - Simon Cliche
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada
| | - Hassan Sabik
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada
| | - Claude Gariépy
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada
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28
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Capko C, Thiessen J, Harach L, Fraser JL, Franklin MT, Abram PK. A method for sampling parasitized Drosophila suzukii (Diptera: Drosophilidae) puparia from soil. J Insect Sci 2024; 24:14. [PMID: 38402603 PMCID: PMC10894651 DOI: 10.1093/jisesa/ieae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/12/2023] [Accepted: 02/05/2024] [Indexed: 02/27/2024]
Abstract
Methods to measure the diversity and biological control impact of parasitoids for the control of spotted-wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) are being developed in support of biological control programs around the world. Existing methods to determine parasitism levels and parasitoid species composition focus on sampling D. suzukii within fresh and rotting fruit. However, many D. suzukii pupate in the soil or in dropped fruit, where additional parasitism could occur and where their parasitoids are thought to overwinter. Here we introduce a method for extracting parasitized D. suzukii puparia from the soil through a sieve and flotation system, allowing for effective collection of puparia, from which parasitoids can then be reared. Although the method considerably underestimates the absolute number of puparia in soil samples, it nonetheless yields a high number of puparia relative to sampling effort and provides a robust estimate of the relative abundance of puparia among samples. Using this method, we confirmed that at least 5 species of parasitoids, including some that have rarely been detected in past studies, overwinter in their immature stages inside D. suzukii puparia in south coastal British Columbia, Canada. The ability to sample puparia from the soil will lead to a more comprehensive view of both D. suzukii and parasitoid abundance throughout the season, help confirm parasitoid establishment following intentional releases, and provide a way to measure the diversity of parasitoid species and potential interactions among parasitoids (e.g., hyper- or klepto-parasitism) that may often occur on the soil surface.
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Affiliation(s)
- Clarissa Capko
- Department of Biology, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
| | - Jason Thiessen
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
| | - Lana Harach
- Department of Biology, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
- Department of Agriculture, University of the Fraser Valley, Chilliwack, BC, V2R 5X6, Canada
| | - Jessica L Fraser
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Pavillon Envirotron, Québec, QC G1V 0A6, Canada
| | - Michelle T Franklin
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
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Wilson AG, Lapen DR, Provencher JF, Wilson S. The role of species ecology in predicting Toxoplasma gondii prevalence in wild and domesticated mammals globally. PLoS Pathog 2024; 20:e1011908. [PMID: 38198498 PMCID: PMC10805296 DOI: 10.1371/journal.ppat.1011908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/23/2024] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Macroecological approaches can provide valuable insight into the epidemiology of globally distributed, multi-host pathogens. Toxoplasma gondii is a protozoan that infects any warm-blooded animal, including humans, in almost every habitat worldwide. Toxoplasma gondii infects its hosts through oocysts in the environment, carnivory of tissue cysts within intermediate host prey and vertical transmission. These routes of infection enable specific predictions regarding the ecological and life history traits that should predispose specific taxa to higher exposure and, thus infection rates of T. gondii. Using T. gondii prevalence data compiled from 485 studies representing 533 free-ranging wild mammalian species, we examined how ecological (habitat type, trophic level) and life history (longevity, vagility, gestation duration and torpor) traits influence T. gondii infection globally. We also compared T. gondii prevalence between wild and domesticated species from the same taxonomic families using data compiled from 540 studies of domestic cattle, sheep, and pigs. Across free-ranging wildlife, we found the average T. gondii prevalence was 22%, which is comparable to the global human estimate. Among ecological guilds, terrestrial species had lower T. gondii prevalence than aquatic species, with freshwater aquatic taxa having an increased prevalence compared to marine aquatic species. Dietary niches were also influential, with carnivores having an increased risk compared to other trophic feeding groups that have reduced tissue cyst exposure in their diet. With respect to influential life history traits, we found that more vagile wildlife species had higher T. gondii infection rates, perhaps because of the higher cumulative risk of infection during movement through areas with varying T. gondii environmental loads. Domestic farmed species had a higher T. gondii prevalence compared to free-ranging confamilial wildlife species. Through a macroecological approach, we determined the relative significance of transmission routes of a generalist pathogen, demonstrating an increased infection risk for aquatic and carnivorous species and highlighting the importance of preventing pathogen pollution into aquatic environments. Toxoplasma gondii is increasingly understood to be primarily an anthropogenically-associated pathogen whose dissemination is enhanced by ecosystem degradation and human subsidisation of free-roaming domestic cats. Adopting an ecosystem restoration approach to reduce one of the world's most common parasites would synergistically contribute to other initiatives in conservation, feline and wildlife welfare, climate change, food security and public health.
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Affiliation(s)
- Amy G. Wilson
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - David R. Lapen
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, Ottawa Research Development Centre, Ottawa, Ontario, Canada
| | - Jennifer F. Provencher
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
| | - Scott Wilson
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Wildlife Research Division, Environment and Climate Change, Pacific Wildlife Research Centre, Delta, British Columbia, Canada
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Kurose D, Seier MK, Evans HC. Exploiting exotic pathogens as mycoherbicides against invasive alien weeds: Japanese knotweed as a case study. Pest Manag Sci 2024; 80:87-91. [PMID: 37086042 DOI: 10.1002/ps.7510] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/22/2023] [Indexed: 05/03/2023]
Abstract
Plant species have been introduced increasingly into non-native ranges, where many have become exotic weeds with adverse impacts on native ecosystems, as well as on farming and other livelihoods. In biological control, the classical or inoculative approach is the one most commonly used for the management of invasive alien weeds and is based on the use of co-evolved natural enemies from the native range to control the invasive weed. Typically, the inundative or mycoherbicide approach targets problematic weeds using local plant pathogens that, in the case of introduced species, have 'jumped' onto the exotic host. The leaf-spot fungus, Mycosphaerella polygoni-cuspidati, co-evolved with its host, Reynoutria (Fallopia) japonica (Japanese knotweed), in Japan and has a unique history of being investigated both as a classical biological control agent and a mycoherbicide against this highly invasive weed in the United Kingdom and North America. Here, we highlight our research on M. polygoni-cuspidati as part of a biological control programme for Japanese knotweed and review the potential of mycoherbicides using exotic pathogens for the management of invasive alien weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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MacInnis CI, Luong LT, Pernal SF. A tale of two parasites: Responses of honey bees infected with Nosema ceranae and Lotmaria passim. Sci Rep 2023; 13:22515. [PMID: 38110440 PMCID: PMC10728187 DOI: 10.1038/s41598-023-49189-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
Nosema ceranae and Lotmaria passim are two commonly encountered digestive tract parasites of the honey bee that have been associated with colony losses in Canada, the United States, and Europe. Though honey bees can be co-infected with these parasites, we still lack basic information regarding how they impact bee health at the individual and colony level. Using locally-isolated parasite strains, we investigated the effect of single and co-infections of these parasites on individual honey bee survival, and their responsiveness to sucrose. Results showed that a single N. ceranae infection is more virulent than both single L. passim infections and co-infections. Honey bees singly infected with N. ceranae reached < 50% survival eight days earlier than those inoculated with L. passim alone, and four days earlier than those inoculated with both parasites. Honey bees infected with either one, or both, parasites had increased responsiveness to sucrose compared to uninfected bees, which could correspond to higher levels of hunger and increased energetic stress. Together, these findings suggest that N. ceranae and L. passim pose threats to bee health, and that the beekeeping industry should monitor for both parasites in an effort correlate pathogen status with changes in colony-level productivity and survival.
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Affiliation(s)
- Courtney I MacInnis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB, T0H 0C0, Canada.
| | - Lien T Luong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen F Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB, T0H 0C0, Canada.
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32
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van Herk WG, Warren RL, Bailey T. Wireworm (Coleoptera: Elateridae) intoxication symptoms indicate the postharvest presence of broflanilide residues in soil collected from potato fields. J Econ Entomol 2023; 116:1998-2008. [PMID: 37942675 DOI: 10.1093/jee/toad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Wireworms are primary pests of potatoes in Canada with relatively few effective control options. Recently, a new meta-diamide insecticide, broflanilide, was registered in Canada and the United States as an in-furrow spray applied at planting that provides protection of tubers from feeding damage and dramatically reduces wireworm populations. As part of our routine screening of wireworm response to novel insecticides, we exposed wireworms (predominantly Agriotes obscurus; N=2320) to field soil collected from plots to which either bifenthrin (Capture 2EC) or broflanilide (Cimegra) had been applied at registered rates 124-145 and 314-335 days previously in 2018, 2019, and 2021. Wireworm behavioral responses were assessed using a previously developed numerical scale, and indicated residues were present in sufficient quantity in all broflanilide and most bifenthrin-treated plots to induce morbidity. Transfer of affected wireworms to untreated soil indicated morbidity was generally reversible after exposure to bifenthrin, but not after exposure to broflanilide. There was an inverse relation between wireworm size and the degree of morbidity induced by exposure to broflanilide, but not bifenthrin. Analyses of soil residues indicated readily quantifiable levels of broflanilide still present in undisturbed (not harvested) field soil 314-335 days after application. Insecticide residues in soil samples from disturbed (harvested) sections of the potato plots were lower, as was the degree of morbidity of wireworms exposed to this soil. The use of wireworms as bioindicators of insecticide residues, and the implications of insecticide persistence for wireworm management are discussed.
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Affiliation(s)
- Willem G van Herk
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 1000, Agassiz, BC V0M 1A0, Canada
| | - Ralph L Warren
- BASF Crop Protection, 26 Davis Drive, Research Triangle Park, Raleigh, NC 27709, USA
| | - Terisha Bailey
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 1000, Agassiz, BC V0M 1A0, Canada
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Lue CH, Abram PK, Hrcek J, Buffington ML, Staniczenko PPA. Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research. Mol Ecol 2023; 32:6461-6473. [PMID: 36040418 DOI: 10.1111/mec.16677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio-economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.
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Affiliation(s)
- Chia-Hua Lue
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
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Alves K, Brito LF, Sargolzaei M, Schenkel FS. Genome-wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle. J Anim Breed Genet 2023; 140:624-637. [PMID: 37350080 DOI: 10.1111/jbg.12813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
Non-additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive-by-additive) effects in fertility and reproduction traits in Holstein cattle. Nine fertility and reproduction traits were analysed on 5825 and 6090 Holstein heifers and cows with phenotypes and genotypes, respectively. The Marginal Epistasis Test (MAPIT) was used to identify SNPs with significant marginal epistatic effects at a chromosome-wise 5% and 10% false discovery rate (FDR) level. The -log10 (p) values were adjusted by the genomic inflation factor (λ) to correct for the potential bias on the p-values and minimize the possible effects of population stratification. After adjustments, MAPIT enabled the identification of genomic regions with significant marginal epistatic effects for heifers on BTA5 for age at first insemination, BTA3 and BTA24 for non-return rate (NRR); BTA16 and BTA28 for gestation length (GL); BTA1, BTA4 and BTA17 for stillbirth (SB). For the cow traits, MAPIT enabled the identification of regions on BTA11 for GL, BTA11 and BTA16 for SB and BTA19 for calf size (CZ). An additional approach for mapping epistasis in a genome-wide association study was also proposed, in which the genome scan was performed using estimates of epistatic values as the input pseudo-phenotypes, computed using single-trait animal models. Significant SNPs were identified at the chromosome-wise 5% and 10% FDR levels for all traits. For the heifer traits, significant regions were found on BTA7 for AFS; BTA12 for NRR; BTA14 and BTA19 for GL; BTA19 for calving ease (CE); BTA5, BTA24, BTA25 and in the X chromosome for SB; BTA23 and in the X chromosome for CZ and in the X chromosome for the number of services (NS). For the cow traits, significant regions were found on BTA29 and in the X chromosome for NRR, BTA11, BTA16 and in the X chromosome for SB, BTA2 for GL, BTA28 for CZ, BTA19 for calving to first insemination, and in the X chromosome for NS and first insemination to conception. The results suggest that the epistatic genetic effects are likely due to many loci with a small effect rather than few loci with a large effect and/or a single SNP marker alone do not capture the epistatic effects well. The genomic architecture of fertility and reproduction traits is complex, and these results should be validated in independent dairy cattle populations and using alternative statistical models.
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Affiliation(s)
- Kristen Alves
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Bayer CropScience Inc., Guelph, Ontario, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
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Terry V, Kokkoris V, Villeneuve-Laroche M, Turcu B, Chapman K, Cornell C, Zheng Z, Stefani F, Corradi N. Mycorrhizal response of Solanum tuberosum to homokaryotic versus dikaryotic arbuscular mycorrhizal fungi. Mycorrhiza 2023; 33:333-344. [PMID: 37572110 DOI: 10.1007/s00572-023-01123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts of most land plants. In these organisms, thousands of nuclei that are either genetically similar (homokaryotic) or derived from two distinct parents (dikaryotic) co-exist in a large syncytium. Here, we investigated the impact of these two nuclear organizations on the mycorrhizal response of potatoes (Solanum tuberosum) by inoculating four potato cultivars with eight Rhizophagus irregularis strains individually (four homokaryotic and four dikaryotic). By evaluating plant and fungal fitness-related traits four months post inoculation, we found that AMF genetic organization significantly affects the mycorrhizal response of host plants. Specifically, homokaryotic strains lead to higher total, shoot, and tuber biomass and a higher number of tubers, compared to dikaryotic strains. However, fungal fitness-related traits showed no clear differences between homokaryotic and dikaryotic strains. Nucleotype content analysis of single spores confirmed that the nucleotype ratio of AMF heterokaryon spores can shift depending on host identity. Together, these findings continue to highlight significant ecological differences derived from the two distinct genetic organizations in AMF.
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Affiliation(s)
- Victoria Terry
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Present address: Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Present address: Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | | | - Bianca Turcu
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Kendyll Chapman
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Calvin Cornell
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Zhiming Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Franck Stefani
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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Hong GAT, Tobalske BW, van Staaveren N, Leishman EM, Widowski TM, Powers DR, Harlander-Matauschek A. Reduction of wing area affects estimated stress in the primary flight muscles of chickens. R Soc Open Sci 2023; 10:230817. [PMID: 38034124 PMCID: PMC10685109 DOI: 10.1098/rsos.230817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
In flying birds, the pectoralis (PECT) and supracoracoideus (SUPRA) generate most of the power required for flight, while the wing feathers create the aerodynamic forces. However, in domestic laying hens, little is known about the architectural properties of these muscles and the forces the wings produce. As housing space increases for commercial laying hens, understanding these properties is important for assuring safe locomotion. We tested the effects of wing area loss on mass, physiological cross-sectional area (PCSA), and estimated muscle stress (EMS) of the PECT and SUPRA in white-feathered laying hens. Treatments included Unclipped (N = 18), Half-Clipped with primaries removed (N = 18) and Fully-Clipped with the primaries and secondaries removed (N = 18). The mass and PCSA of the PECT and SUPRA did not vary significantly with treatment. Thus, laying hen muscle anatomy may be relatively resistant to changes in external wing morphology. We observed significant differences in EMS among treatments, as Unclipped birds exhibited the greatest EMS. This suggests that intact wings provide the greatest stimulus of external force for the primary flight muscles.
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Affiliation(s)
- Grace A. T. Hong
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
| | - Bret W. Tobalske
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Nienke van Staaveren
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
- Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
| | - Emily M. Leishman
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
| | - Tina M. Widowski
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
| | - Donald R. Powers
- Department of Biology, George Fox University, 414N Meridian St, Newberg, OR 97132, USA
| | - Alexandra Harlander-Matauschek
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario Canada, N1G 2W1
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Da Ros L, Bollina V, Soolanayakanahally R, Pahari S, Elferjani R, Kulkarni M, Vaid N, Risseuw E, Cram D, Pasha A, Esteban E, Konkin D, Provart N, Nambara E, Kagale S. Multi-omics atlas of combinatorial abiotic stress responses in wheat. Plant J 2023; 116:1118-1135. [PMID: 37248640 DOI: 10.1111/tpj.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/10/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Field-grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is required to meet future crop production needs. Here, we employed a systems biology approach in wheat (Triticum aestivum L.) to investigate physio-metabolic adjustments and transcriptome reprogramming involved in acclimations to heat, drought, salinity and all combinations therein. A significant shift in magnitude and complexity of plant response was evident across stress scenarios based on the agronomic losses, increased proline concentrations and 8.7-fold increase in unique differentially expressed transcripts (DETs) observed under the triple stress condition. Transcriptome data from all stress treatments were assembled into an online, open access eFP browser for visualizing gene expression during abiotic stress. Weighted gene co-expression network analysis revealed 152 hub genes of which 32% contained the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) transcriptional repression motif. Cross-referencing against the 31 DETs common to all stress treatments isolated TaWRKY33 as a leading candidate for greater plant tolerance to combinatorial stresses. Integration of our findings with available literature on gene functional characterization allowed us to further suggest flexible gene combinations for future adaptive gene stacking in wheat. Our approach demonstrates the strength of robust multi-omics-based data resources for gene discovery in complex environmental conditions. Accessibility of such datasets will promote cross-validation of candidate genes across studies and aid in accelerating causal gene validation for crop resiliency.
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Affiliation(s)
- Letitia Da Ros
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Venkatesh Bollina
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Raed Elferjani
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Manoj Kulkarni
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Eddy Risseuw
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
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Thomas DJ, Shafiee M, Nosworthy MG, Lane G, Ramdath DD, Vatanparast H. Unveiling the Evidence for the Use of Pulses in Managing Type 2 Diabetes Mellitus: A Scoping Review. Nutrients 2023; 15:4222. [PMID: 37836506 PMCID: PMC10574713 DOI: 10.3390/nu15194222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Management of type 2 diabetes mellitus (T2DM) is a pressing global healthcare challenge. Innovative strategies that integrate superior medical and nutritional practices are essential for holistic care. As such, pulse consumption is encouraged for its potential benefit in reducing hypercholesterolaemia, dyslipidaemia, and triglyceride levels, as well as enhancing glycaemic control. This scoping review aims to assess the depth of evidence supporting the recommendation for pulse consumption in T2DM management and to identify gaps in the existing literature. We conducted a comprehensive search across the databases MEDLINE, Global Health, EMBASE, CINAHL, Web of Science, and the Cochrane Library (up to July 2023). We included population-based studies of any design, and excluded review-style articles. Articles published in languages other than English were also excluded. From the 2449 studies initially identified, 28 met our inclusion criteria. Acute postprandial trials demonstrated improved glucose responses and enhanced insulin responses to pulse-based intervention. Meanwhile, long-term trials reported meaningful improvements in T2DM indicators such as haemoglobin A1C (HbA1c), fasting glucose, fasting insulin, C-peptide, and markers of insulin resistance like homeostatic model assessment (HOMA). Integrating more pulses into the diets of diabetic individuals might offer an efficient and cost-effective strategy in the global initiative to combat T2DM.
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Affiliation(s)
- Daniel J. Thomas
- Caribbean Institute for Health Research, The University of the West Indies, Mona, Kingston 7, Jamaica;
- School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada
| | - Mojtaba Shafiee
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada; (M.S.); (M.G.N.)
| | - Matthew G. Nosworthy
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada; (M.S.); (M.G.N.)
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Ginny Lane
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - D. Dan Ramdath
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada; (M.S.); (M.G.N.)
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Hassan Vatanparast
- School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada; (M.S.); (M.G.N.)
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Macrae ML, Plach JM, Carlow R, Little C, Jarvie HP, McKague K, Pluer WT, Joosse P. Trade-offs in nutrient and sediment losses in tile drainage from no-till versus conventional conservation-till cropping systems. J Environ Qual 2023; 52:1011-1023. [PMID: 37449773 DOI: 10.1002/jeq2.20502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
Nutrient and soil loss from agricultural areas impairs surface water quality globally. In the Great Lakes region, increases in the frequency and magnitude of harmful and nuisance algal blooms in freshwater lakes have been linked to elevated phosphorus (P) losses from agricultural fields, some of which are transported via tile drainage. This study examined whether concentrations and loads of P fractions, total suspended sediments (TSS), nitrate (NO3 - ), and ammonium (NH4 + ) in tile drainage in a clay soil differed between a continuous no-till system combining cover crops and surface broadcast fertilizer (no-till cover crop [NTCC]), and a more conventional tillage system with shallow tillage, fertilizer incorporation and limited use of cover crops (conventional conservation-till, CT). Both sites had modest soil fertility levels. Year-round, high-frequency observations of tile drainage flow and chemistry are described over 4 full water years and related to management practices on the associated fields. There were similar water yields in tile drainage between the two systems; however, losses of TSS, particulate P (PP), and NO3 - were consistently greater from the CT site, which received larger quantities of fertilizer. In contrast, dissolved reactive P (DRP) losses were considerably greater from the NTCC site, offsetting the lower PP losses, such that there was little difference in TP losses between sites. Approximately 60% of the DRP losses from the NTCC site over the 4 years were associated with incidental losses following surface application of fertilizer in fall. This study provides insight into trade-offs in controlling losses of different nutrient fractions using different management systems.
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Affiliation(s)
- M L Macrae
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, Ontario, Canada
| | - J M Plach
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, Ontario, Canada
| | - R Carlow
- Lower Thames Valley Conservation Authority, Chatham, Ontario, Canada
| | - C Little
- Lower Thames Valley Conservation Authority, Chatham, Ontario, Canada
| | - H P Jarvie
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, Ontario, Canada
| | - K McKague
- Ontario Ministry of Agriculture, Food and Rural Affairs, Woodstock, Ontario, Canada
| | - W T Pluer
- Elon University, Elon, North Carolina, USA
| | - P Joosse
- Agriculture and Agri-food Canada, Guelph, Ontario, Canada
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40
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Ban Z, Fan L, Song J, Fillmore S, Guan J. Antibacterial Effect of Pomegranate Juice on Listeria innocua and E. coli in Different Media. Foods 2023; 12:3247. [PMID: 37685180 PMCID: PMC10487088 DOI: 10.3390/foods12173247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
The antibacterial effect of pomegranate juice (PJ) at six concentrations (0, 10, 20, 30, 40, and 50%) against Listeria innocua and Escherichia coli was investigated in distilled water (DW) and bacterial culture broth. L. innocua and E. coli at approximately 105 cfu mL-1 were inoculated in PJ samples and incubated at 4, 25, and 37 °C for 0, 6, 24, and 48 h. The bacterial population and pH of culture media were measured at each removal. Results indicated that the antibacterial effect of PJ was dependent upon bacteria species, juice concentration, incubation temperature, and growth medium. Higher juice concentration and incubation temperature resulted in increased antibacterial effects. Bacterial populations were decreased more significantly in DW systems than in the culture broth, while L. innocua was more sensitive to PJ than E. coli in the DW systems. Regardless of PJ concentrations in DW systems, L. innocua, initially inoculated at approximately 105 cfu mL-1, was reduced to undetectable levels at 25 and 37 °C within 24 h. The growth of L. innocua and E. coli was significantly inhibited in bacterial culture broth containing ≥ 20% PJ (p < 0.001). This study provides insight into the potential application of PJ in food and beverage products for food protection.
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Affiliation(s)
- Zhaojun Ban
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Lihua Fan
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada; (J.S.); (S.F.)
| | - Jun Song
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada; (J.S.); (S.F.)
| | - Sherry Fillmore
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada; (J.S.); (S.F.)
| | - Junfeng Guan
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050050, China;
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41
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Chen W, Modi D, Picot A. Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review. Plants (Basel) 2023; 12:2736. [PMID: 37514350 PMCID: PMC10384710 DOI: 10.3390/plants12142736] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dixi Modi
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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42
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Dawdani S, O'Neill M, Castillo C, Sámano JEM, Higo H, Ibrahim A, Pernal SF, Plettner E. Effects of dialkoxybenzenes against Varroa destructor and identification of 1-allyloxy-4-propoxybenzene as a promising acaricide candidate. Sci Rep 2023; 13:11195. [PMID: 37433810 DOI: 10.1038/s41598-023-38187-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/04/2023] [Indexed: 07/13/2023] Open
Abstract
The honey bee is responsible for pollination of a large proportion of crop plants, but the health of honey bee populations has been challenged by the parasitic mite Varroa destructor. Mite infestation is the main cause of colony losses during the winter months, which causes significant economic challenges in apiculture. Treatments have been developed to control the spread of varroa. However, many of these treatments are no longer effective due to acaricide resistance. In a search of varroa-active compounds, we tested the effect of dialkoxybenzenes on the mite. A structure-activity relationship revealed that 1-allyloxy-4-propoxybenzene is most active of a series of dialkoxybenzenes tested. We found that three compounds (1-allyloxy-4-propoxybenzene, 1,4-diallyloxybenzene and 1,4-dipropoxybenzene) cause paralysis and death of adult varroa mites, whereas the previously discovered compound, 1,3-diethoxybenzene, which alters host choice of adult mites in certain conditions, did not cause paralysis. Since paralysis can be caused by inhibition of acetylcholinesterase (AChE), a ubiquitous enzyme in the nervous system of animals, we tested dialkoxybenzenes on human, honey bee and varroa AChE. These tests revealed that 1-allyloxy-4-propoxybenzene had no effects on AChE, which leads us to conclude that 1-allyloxy-4-propoxybenzene does not exert its paralytic effect on mites through AChE. In addition to paralysis, the most active compounds affected the ability of the mites to find and remain at the abdomen of host bees provided during assays. A test of 1-allyloxy-4-propoxybenzene in the field, during the autumn of 2019 in two locations, showed that this compound has promise in the treatment of varroa infestations.
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Affiliation(s)
- Soniya Dawdani
- Department of Chemistry, Simon Fraser University, 8888 Univ. Dr., Burnaby, BC, V5A 1S6, Canada
| | - Marissa O'Neill
- Department of Chemistry, Simon Fraser University, 8888 Univ. Dr., Burnaby, BC, V5A 1S6, Canada
| | - Carlos Castillo
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB, T0H 0C0, Canada
| | - Jorge E Macias Sámano
- Department of Chemistry, Simon Fraser University, 8888 Univ. Dr., Burnaby, BC, V5A 1S6, Canada
| | - Heather Higo
- Department of Chemistry, Simon Fraser University, 8888 Univ. Dr., Burnaby, BC, V5A 1S6, Canada
| | - Abdullah Ibrahim
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB, T0H 0C0, Canada
| | - Stephen F Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, P.O. Box 29, Beaverlodge, AB, T0H 0C0, Canada
| | - Erika Plettner
- Department of Chemistry, Simon Fraser University, 8888 Univ. Dr., Burnaby, BC, V5A 1S6, Canada.
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DesRochers N, Renaud JB, Tanney JB, Ibrahim A, Yeung KKC, Sumarah MW. Non-targeted Screening of Natural Products from 288 Fungal Endophytes from Canadian Fruit Crops. ACS Omega 2023; 8:24561-24572. [PMID: 37457466 PMCID: PMC10339433 DOI: 10.1021/acsomega.3c02786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Many diverse species of fungi naturally occur as endophytes in plants. The majority of these fungi produce secondary metabolites of diverse structures and biological activities. Culture extracts from 288 fungi isolated from surface-sterilized blueberries, cranberries, raspberries, and grapes were analyzed by LC-HRMS/MS. Global Natural Products Social (GNPS) Molecular Networking modeling was used to investigate the secondary metabolites in the extracts. This technique increased the speed and simplicity of dereplicating the extracts, targeting new compounds that are structurally related. In total, 60 known compounds were dereplicated from this collection and seven new compounds were identified. These previously unknown compounds are targets for purification, characterization, and bioactivity testing in future studies. The fungal endophytes characterized in this study are potential candidates for providing bio-protection to the host plant with a reduced reliance on chemical pesticides.
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Affiliation(s)
- Natasha DesRochers
- London
Research and Development Centre, Agriculture
and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
- Department
of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Justin B. Renaud
- London
Research and Development Centre, Agriculture
and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
| | - Joey B. Tanney
- Pacific
Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Ashraf Ibrahim
- McMaster
University, 1290 Main
St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Ken K.-C. Yeung
- Department
of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
- Department
of Biochemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Mark W. Sumarah
- London
Research and Development Centre, Agriculture
and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
- Department
of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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44
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Kalbe C, Metzger K, Gariépy C, Palin MF. Effect of muscle fibre types and carnosine levels on the expression of carnosine-related genes in pig skeletal muscle. Histochem Cell Biol 2023; 160:63-77. [PMID: 37171629 PMCID: PMC10313551 DOI: 10.1007/s00418-023-02193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2023] [Indexed: 05/13/2023]
Abstract
It is generally accepted that carnosine (β-alanyl-L-histidine) content is higher in glycolytic than in oxidative muscle fibres, but the underlying mechanisms responsible for this difference remain to be elucidated. A first study to better understand potential mechanisms involved was undertaken (1) to determine whether differences in the expression of carnosine-related enzymes (CARNS1, CNDP2) and transporters (SLC6A6, SLC15A3, SLC15A4, SLC36A1) exist between oxidative and glycolytic myofibres and (2) to study the effect of carnosine on myoblast proliferative growth and on carnosine-related gene expression in cultured myoblasts isolated from glycolytic and oxidative muscles. Immunohistochemistry analyses were conducted to determine the cellular localization of carnosine-related proteins. Laser-capture microdissection and qPCR analyses were performed to measure the expression of carnosine-related genes in different myofibres isolated from the longissimus dorsi muscle of ten crossbred pigs. Myogenic cells originating from glycolytic and oxidative muscles were cultured to assess the effect of carnosine (0, 10, 25 and 50 mM) on their proliferative growth and on carnosine-related gene expression. The mRNA abundance of CNDP2 and of the studied carnosine transporters was higher in oxidative than in glycolytic myofibres. Since carnosine synthase (CARNS1) mRNA abundance was not affected by either the fibre type or the addition of carnosine to myoblasts, its transcriptional regulation would not be the main process by which carnosine content differences are determined in oxidative and glycolytic muscles. The addition of carnosine to myoblasts leading to a dose-dependent increase in SLC15A3 transcripts, however, suggests a role for this transporter in carnosine uptake and/or efflux to maintain cellular homeostasis.
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Affiliation(s)
- Claudia Kalbe
- Research Institute for Farm Animal Biology, Institute of Muscle Biology and Growth, Dummerstorf, Germany
| | - Katharina Metzger
- Research Institute for Farm Animal Biology, Institute of Behavioural Physiology, Dummerstorf, Germany
| | - Claude Gariépy
- Agriculture and Agri-Food Canada, St-Hyacinthe Research and Development Centre, St-Hyacinthe, QC, Canada
| | - Marie-France Palin
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.
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Abstract
Climate change is increasingly affecting agriculture through droughts, high salinity in soils, heatwaves, and floodings, which put intense pressure on crops. This results in yield losses, leading to food insecurity in the most affected regions. Multiple plant-beneficial bacteria belonging to the genus Pseudomonas have been shown to improve plant tolerance to these stresses. Various mechanisms are involved, including alteration of the plant ethylene levels, direct phytohormone production, emission of volatile organic compounds, reinforcement of the root apoplast barriers, and exopolysaccharide biosynthesis. In this review, we summarize the effects of climate change-induced stresses on plants and detail the mechanisms used by plant-beneficial Pseudomonas strains to alleviate them. Recommendations are made to promote targeted research on the stress-alleviating potential of these bacteria.
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46
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Bromfield ESP, Cloutier S, Hynes MF. Ensifer canadensis sp. nov. strain T173 T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae. Front Microbiol 2023; 14:1195755. [PMID: 37389331 PMCID: PMC10306167 DOI: 10.3389/fmicb.2023.1195755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/09/2023] [Indexed: 07/01/2023] Open
Abstract
A bacterial strain, designated T173T, was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173T was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173T. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173T in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04T as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173T compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173T has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173T. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173T. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173T (= LMG 32374T = HAMBI 3766T) as the species type strain.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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47
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Rakotoarinia MR, Seidou O, Lapen DR, Leighton PA, Ogden NH, Ludwig A. Future land-use change predictions using Dyna-Clue to support mosquito-borne disease risk assessment. Environ Monit Assess 2023; 195:815. [PMID: 37286856 PMCID: PMC10246872 DOI: 10.1007/s10661-023-11394-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
Mosquitoes are known vectors for viral diseases in Canada, and their distribution is driven by climate and land use. Despite that, future land-use changes have not yet been used as a driver in mosquito distribution models in North America. In this paper, we developed land-use change projections designed to address mosquito-borne disease (MBD) prediction in a 38 761 km2 area of Eastern Ontario. The landscape in the study area is marked by urbanization and intensive agriculture and hosts a diverse mosquito community. The Dyna-CLUE model was used to project land-use for three time horizons (2030, 2050, and 2070) based on historical trends (from 2014 to 2020) for water, forest, agriculture, and urban land uses. Five scenarios were generated to reflect urbanization, agricultural expansion, and natural areas. An ensemble of thirty simulations per scenario was run to account for land-use conversion uncertainty. The simulation closest to the average map generated was selected to represent the scenario. A concordance matrix generated using map pair analysis showed a good agreement between the simulated 2020 maps and 2020 observed map. By 2050, the most significant changes are predicted to occur mainly in the southeastern region's rural and forested areas. By 2070, high deforestation is expected in the central west. These results will be integrated into risk models predicting mosquito distribution to study the possibility of humans' increased exposure risk to MBDs.
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Affiliation(s)
- Miarisoa Rindra Rakotoarinia
- Département de Pathologie Et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada.
- Groupe de Recherche en Épidémiologie Des Zoonoses Et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada.
| | - Ousmane Seidou
- Department of Civil Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Patrick A Leighton
- Département de Pathologie Et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Groupe de Recherche en Épidémiologie Des Zoonoses Et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - Nicholas H Ogden
- Groupe de Recherche en Épidémiologie Des Zoonoses Et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 3190 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - Antoinette Ludwig
- Groupe de Recherche en Épidémiologie Des Zoonoses Et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 3190 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
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48
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Abram PK, Haye T, Clarke P, Grove E, Thiessen J, Gariepy TD. Partial refuges from biological control due to intraspecific variation in protective host traits. Ecol Appl 2023; 33:e2796. [PMID: 36502297 DOI: 10.1002/eap.2796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 06/02/2023]
Abstract
Predicting how much of a host or prey population may be attacked by their natural enemies is fundamental to several subfields of applied ecology, particularly biological control of pest organisms. Hosts or prey can occupy refuges that prevent them from being killed by natural enemies, but habitat or ecological refuges are challenging or impossible to predict in a laboratory setting-which is often where efficacy and specificity testing of candidate biological control agents is done. Here we explore how intraspecific variation in continuous traits of individuals or groups that confer some protection from natural enemy attack-even after the natural enemy has encountered the prey-could provide partial refuges. The size of these trait-based refuges (i.e., the proportion of prey that survive natural enemy encounters due to protective traits) should depend on the relationship between trait values and host/prey susceptibility to natural enemy attack and on how common different trait values are within a host/prey population. These can be readily estimated in laboratory testing of natural enemy impact on target or nontarget prey or hosts as long as sufficient host material is available. We provide a general framework for how intraspecific variation in protective host traits could be integrated into biological control research, specifically with reference to nontarget testing as part of classical biological control programs. As a case study, we exposed different host clutch sizes of target (pest) and nontarget (native species) stink bug (Hemiptera: Pentatomidae) species to a well-studied exotic biocontrol agent, the egg parasitoid Trissolcus japonicus (Hymenoptera: Scelionidae). We predicted that the smallest and largest clutches would occupy trait-based refuges from parasitism. Although we observed several behavioral and reproductive responses to variation in host egg mass size by T. japonicus, they did not translate to increases in host survival large enough to change the conclusions of nontarget testing. We encourage researchers to investigate intraspecific variation in a wider variety of protective host and prey traits and their consequences for refuge size.
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Affiliation(s)
- Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | | | - Peggy Clarke
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Emily Grove
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jason Thiessen
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Tara D Gariepy
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
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49
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Dettman JR, Eggertson QA, Kim NE. Species diversity and molecular characterization of Alternaria section Alternaria isolates collected mainly from cereal crops in Canada. Front Microbiol 2023; 14:1194911. [PMID: 37303811 PMCID: PMC10249498 DOI: 10.3389/fmicb.2023.1194911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
Alternaria is often one on the most abundant fungal genera recovered from a wide array of plant hosts and environmental substrates. Many species within the sub-generic Alternaria section Alternaria are common plant pathogens that cause pre-harvest losses due to reduced productivity and post-harvest losses due to spoilage and contamination with mycotoxins. As certain species of Alternaria may have distinct mycotoxin profiles, and very broad host ranges, understanding the distribution of species by geography and host is critical for disease prediction, toxicological risk assessment, and guiding regulatory decisions. In two previous reports, we performed phylogenomic analyses to identify highly informative molecular markers for Alternaria section Alternaria, and validated their diagnostic ability. Here, we perform molecular characterization of 558 section Alternaria strains, collected from 64 host genera in 12 countries, using two of these section-specific loci (ASA-10 and ASA-19) along with the RNA polymerase II second largest subunit (rpb2) gene. The majority of strains (57.4%) originated from various cereal crops in Canada, which formed the main focus of our study. Phylogenetic analyses were used to classify strains into section Alternaria species/lineages, demonstrating that the most common species on Canadian cereal crops are Alternaria alternata and A. arborescens. Further population genetic analyses were consistent with A. alternata being a widely distributed species with relatively low levels of geographic isolation (i.e., Canadian isolates did not form distinct clades when compared to other regions). Our expanded sampling of A. arborescens has greatly increased the known diversity of this group, with A. arborescens isolates forming at least three distinct phylogenetic lineages. Proportionally, A. arborescens is more prevalent in Eastern Canada than in Western Canada. Sequence analyses, putative hybrids, and mating-type distributions provided some evidence for recombination events, both within and between species. There was little evidence for associations between hosts and genetic haplotypes of A. alternata or A. arborescens.
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Ajeethan N, Ali S, Fuller KD, Abbey L, Yurgel SN. Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils. Microorganisms 2023; 11:1372. [PMID: 37374874 DOI: 10.3390/microorganisms11061372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A study was performed using 16S rRNA/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to assess soil- and root-associated microbiomes, respectively, from mature apple orchards and soil microbiomes alone from uncultivated soil. The results indicated significant (p < 0.05) differences in soil microbial community structure and composition between uncultivated soil and cultivated apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil. At the same time, we detected a significant (p < 0.05) increase in relative abundances of several potential plant-growth-promoting or biocontrol microorganisms and non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soils. Additionally, the apple roots accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Nectriaceae and plant pathogenic Fusarium spp., were decreased in the apple root microbiome compared to the soil microbiome. The results suggest that the health of a mature apple tree can be ascribed to a complex interaction between potential pathogenic and plant growth-promoting microorganisms in the soil and on apple roots.
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Affiliation(s)
- Nivethika Ajeethan
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
- Department of Biosystems Technology, Faculty of Technology, University of Jaffna, Kilinochchi 44000, Sri Lanka
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Keith D Fuller
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
| | - Svetlana N Yurgel
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
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